In order to bioinformaticly show DEGs of RNA-seq in a volcano plot, I intend to use R, showing DEGs with blue spots and not significantly expressed genes with red dots.

The edgeR package which is embedded in Trinity software, uses FDR (>0.001) and log2FC (>2) of the matrix file as the threshold.

I will show my R code and the head of my matrix file. My QUESTIONs are:

1- Which I should use, FDR or -log10(FDR) ? (e.g in aes(x=logFC, y =-log10(FDR),) (when I used FDR the volcano was funny and when I used -10log(FDR), it seems that the number of blue dots that are presenting the DEGs are more than number of DEGs reported by Trinity package.

I think your logFC values are is already log2. In general, volcano plots are logFC vs P-value (-logged (10), in most cases). There are manuscripts that used FDR in volcano plots. Almost similar post here: Volcano plot p-value or FDR?

It makes sense (to me) to use -log10 (FDR) instead of FDR. Talk to your PI or client or the intended journal, once you are done with it and iterate it as per the feedback. Please label the axis accordingly.